The answer should be determined on a case by case basis, but I will outline some things to consider below; of course I welcome the community to provide their expert input on this subject as well.
Pros:
-Eliminate the need to do layout on the PCB; considering that DDR memory is one of the hardest interfaces to get right, this is a huge advantage
-We do (Samsung) and/or will (Micron) provide software to support POP memory.
Cons:
-Rather new process: many not be very well supported by some fabs, also Samsung and Micron are the two primary companies driving this
-There are likely additional costs with this approach from fabs.
-Although both vendors (Samsung and Micron) have suggested support for these devices for many years to come, they have stopped short of issuing a blanket statement; therefore, customers should seek an agreement with the corresponding company once the device has been selected.